Molecular Biology

, Volume 34, Issue 6, pp 823–839 | Cite as

Photoactivatable Reagents Based on Aryl(trifluoromethyl)diazirines: Synthesis and Application for Studying Nucleic Acid–Protein Interactions

  • G. A. Korshunova
  • N. V. Sumbatyan
  • A. N. Topin
  • M. T. Mtchedlidze
Article

Abstract

Recent data on the synthesis of photoactivatable derivatives of nucleic acids and proteins on the basis of aryl(trifluoromethyl)diazirines—analogs of nucleosides, nucleotides, oligonucleotides, as well as amino acids and peptides—are reviewed. The synthesis of bi- and polyfunctional photoactivatable reagents, including those containing a cleavable function, designed for postsynthetic modification of biopolymers is described. Data are given on the use of the photoactivatable derivatives for studying nucleic acid–protein interactions by the method of photoaffinity labeling. Special consideration is paid to the results obtained by the authors" team in cooperation with other researchers as well as graduate students of the Chemistry of Natural Products Chair, Chemical Faculty, Moscow State University and destined to solve various scientific tasks in the domain of nucleic acid–protein recognition with the use of photoaffinity crosslinking.

aryl(trifluoromethyl)diazirine photoactivatable nucleosides and nucleotides bi- and polyfunctional photoreagents cleavable photoreagents photoaffinity crosslinking nucleic acid–protein interactions. 

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REFERENCES

  1. 1.
    Singh, A., Thornton, E.R., and Westheimer, F.H., J. Biol. Chem., 1962, vol. 237, pp. 3006–3008.PubMedGoogle Scholar
  2. 2.
    Bayley, H., Photogenerated Reagents in Biochemistry and Molecular Biology, Work, T. and Burdon, R., Eds., Amsterdam: Elsevier, 1983, vol. 12, p. 187.Google Scholar
  3. 3.
    Brunner, J., Annu. Rev. Biochem., 1993, vol. 62, pp. 483–514.PubMedGoogle Scholar
  4. 4.
    Kotzyba-Hilbert, F., Kapfer, I., and Goedner, M., Angew. Chem., Int. Ed., 1995, vol. 34, pp. 1296–1312.Google Scholar
  5. 5.
    Sheflyan, G.Ya., Kubareva, E.A., and Gromova, E.S., Usp. Khim., 1996, vol. 65, no. 8, pp. 765–780.Google Scholar
  6. 6.
    Knorre, D.G. and Godovikova, T.S., FEBS Lett., 1998, vol. 433, pp. 9–14.PubMedGoogle Scholar
  7. 7.
    Fleming, S.A., Tetrahedron, 1995, vol. 51, pp. 12479–12520.CrossRefGoogle Scholar
  8. 8.
    Meisenheimer, K.M. and Koch, T.H., Crit. Rev. Biochem. Mol. Biol., 1997, vol. 32, pp. 101–140.PubMedGoogle Scholar
  9. 9.
    Dobrikov, M.I., Zarytova, V.F., Komarova, N.I., Levina, A.S., Lokhov, S.A., Prikhod'ko, T.A., Shishkin, G.V., Tabatadze, D.R., and Zaalishvili, M.M., Bioorg. Khim., 1992, vol. 18, pp. 540–549.PubMedGoogle Scholar
  10. 10.
    Dobrikov, M.I., Dudko, R.Yu., Levina, A.S., Khalimskaya, L.M., and Shishkin, G.V., Bioorg. Khim., 1996, vol. 22, pp. 200–207.Google Scholar
  11. 11.
    Kanevskii, I.E. and Kuznetsova, S.A., Usp. Khim., 1998, vol. 67, pp. 688–704.Google Scholar
  12. 12.
    Kolpashchikov, D.M., Zakharenko, A.L., Dezhurov, S.V., Rechkunova, N.I., Khodyreva, S.N., Degtyarev, S.Kh., Litvak, V.V., and Lavrik, O.I., Bioorg. Khim., 1999, vol. 25, pp. 129–136.PubMedGoogle Scholar
  13. 13.
    Favre, A., Bioorganic Photochemistry, Morrison, H., Ed., New York: John Wiley & Sons, 1990, pp. 379–425.Google Scholar
  14. 14.
    Smith, R.A.G. and Knowles, J.R., J. Am. Chem. Soc., 1973, vol. 95, pp. 5072–5073.PubMedGoogle Scholar
  15. 15.
    Bayley, H. and Knowles, J.R., Biochemistry, 1978, vol. 17, pp. 2414–2423.PubMedGoogle Scholar
  16. 16.
    Brunner, J., Senn, H., and Richards, F.M., J. Biol. Chem., 1980, vol. 255, pp. 3313–3318.PubMedGoogle Scholar
  17. 17.
    Brunner, J. and Semenza, G., Biochemistry, 1981, vol. 20, pp. 7174–7182.PubMedGoogle Scholar
  18. 18.
    Nassal, M., Liebigs Ann. Chem., 1983, pp. 1510–1523.Google Scholar
  19. 19.
    Dolder, M., Michei, H., and Sigrist, H., J. Protein Chem., 1990, vol. 9, pp. 407–415.PubMedGoogle Scholar
  20. 20.
    Bayley, H. and Staros, J.V., Azides and Nitrenes, Scriven, E., Ed., New York: Academic, 1984, pp. 433–490.Google Scholar
  21. 21.
    Topin, A.N., Synthesis of Photoactivatable Compounds on the Basis of Aryl(trifluoromethyl)diazirine for the Application in Biological System Studies), Cand. Sci. (Chem.) Dissertation, Moscow: Moscow State Univ., 1996.Google Scholar
  22. 22.
    Brunner, J. and Richards, F., J. Biol. Chem., 1980, vol. 225, pp. 3319–3329.Google Scholar
  23. 23.
    Nakayama, H. and Khorana, G., J. Org. Chem., 1990, vol. 55, pp. 4953–4956.Google Scholar
  24. 24.
    Baldwin, J., Jesudason, C., Moloney, M., Morgan, D., and Pratt, A., Tetrahedron, 1991, vol. 47, pp. 5603–5614.Google Scholar
  25. 25.
    Barton, D., Jaszberenyi, J., Theodorakis, E., and Reibenspies, J., J. Am. Chem. Soc., 1993, vol. 115, pp. 8050–8059.Google Scholar
  26. 26.
    Delfino, J., Schreiber, S., and Richards, F., J. Am. Chem. Soc., 1993, vol. 115, pp. 3458–3474.Google Scholar
  27. 27.
    Rimoldi, J., Kingston, D., Chaudhary, A., Samaranayake, G., Grover, S., and Hamel, E., J. Nat. Prod., 1993, vol. 56, pp. 1313–1330.PubMedGoogle Scholar
  28. 28.
    Ruhmann, A. and Wentrup, C., Tetrahedron, 1994, vol. 50, pp. 3785–3796.Google Scholar
  29. 29.
    Hatanaka, Y., Hashimoto, M., Kurihara, H., Nakayama, H., and Kanaoka, Y., J. Org. Chem., 1994, vol. 59, pp. 383–387.Google Scholar
  30. 30.
    Findlay, J., Fishwick, C., Kersey, I., and Ward, P., Synthesis, 1995, pp. 553–556.Google Scholar
  31. 31.
    Heck, R.F., J. Am. Chem. Soc., 1968, vol. 90, pp. 5518–5525.Google Scholar
  32. 32.
    Bigge, C.F. and Mertes, M.P., J. Org. Chem., 1981, vol. 46, pp. 1994–1997.Google Scholar
  33. 33.
    Chang, G. and Mertes, H., J. Org. Chem., 1987, vol. 52, pp. 3625–3631.Google Scholar
  34. 34.
    Nasonov, A.F. and Korshunova, G.A., Usp. Khim., 1999, vol. 68, pp. 532–554.Google Scholar
  35. 35.
    Yamaguchi, T. and Saneyoshi, M., Nucleosides Nucleotides, 1996, vol. 15, pp. 607–618.Google Scholar
  36. 36.
    Yamaguchi, T. and Saneyoshi, M., Nucleic Acids Res., 1996, vol. 24, pp. 3364–3369.PubMedGoogle Scholar
  37. 37.
    Yamaguchi, T., Suyama, K., Narita, K., Kohgo, S., Tomikawa, A., and Saneyoshi, M., Nucleic Acids Res., 1997, vol. 25, pp. 2352–2358.PubMedGoogle Scholar
  38. 38.
    Agapkin, D.V., Vestn. Mosk. Univ., Ser. 2: Khim., 1999, vol. 40, pp. 207–208.Google Scholar
  39. 39.
    Topin, A.N., Gritsenko, O.V., Brevnov, M.G., Gromova, E.S., and Korshunova, G.A., Nucleosides Nucleotides, 1998, vol. 17, pp. 1163–1175.Google Scholar
  40. 40.
    Bailly, V., Verly, V.G., O'Connor, T.R., and Laval, J., Biochem. J., 1989, vol. 262, pp. 581–589.PubMedGoogle Scholar
  41. 41.
    Donehower, L.A. and Varmus, H.E., Proc. Natl. Acad. Sci. USA, 1984, vol. 81, pp. 6461–6465.PubMedGoogle Scholar
  42. 42.
    Tate, J.J., Persinger, J., and Bartolomew, B., Nucleic Acids Res., 1998, vol. 26, pp. 1421–1426.PubMedGoogle Scholar
  43. 43.
    Korshunova, G.A., Topin, A.N., Sumbatyan, N.V., Koroleva, O.N., and Drutsa, V.L., XIII International Round Table Nucleosides, Nucleotides and Their Biological Applications, Montpellier, 1998, p. 173.Google Scholar
  44. 44.
    Korshunova, G.A., Topin, A.N., Sumbatyan, N.V., Koroleva, O.N., and Drutsa, V.L., Nucleosides Nucleotides, 1999, vol. 18, pp. 1097–1098.Google Scholar
  45. 45.
    Mtchedlidze, M.T., Sumbatyan, N.V., Topin, A.N., Volkov, E.M., and Korshunova, G.A., 7th Ibn Sina International Conference on Pure and Applied Heterocyclic Chemistry, Alexandria, 2000, p. 198.Google Scholar
  46. 46.
    Korshunova, G.A., Krynetski, E.Y., Mtchedlidze, M.T., Agapkin, D.V., Evans, W.E., and Krynetskaya, N.F., Nucleosides Nucleotides, 1999, vol. 18, pp. 1747–1748.PubMedGoogle Scholar
  47. 47.
    Krynetskii, E.Yu., Mol. Biol., 1996, vol. 30, pp. 69–80.Google Scholar
  48. 48.
    Kuznetsova, L.G., Volkov, E.M., Romanova, E.A., Tashlitskii, V.N., Oretskaya, T.S., Krynetskaya, N.F., and Shabarova, Z.A., Bioorg. Khim., 1993, vol. 19, pp. 455–466.PubMedGoogle Scholar
  49. 49.
    Kachalova, A.V. and Zubin, E.M., Dokl. Akad. Nauk, 1998, vol. 363, pp. 507–509.Google Scholar
  50. 50.
    Zubin, E.M., Antsypovich, S.I., Oretskaya, T.S., Romanova, E.A., Volkov, E.M., Tashlitsky, V.N., Dolinnaya, N.G., and Shabarova, Z.A., Nucleosides Nucleotides, 1998, vol. 17, pp. 425–440.Google Scholar
  51. 51.
    Metelev, V.G. and Oretskaya, T.S., Bioorg. Khim., 1999, vol. 25, pp. 474–478.Google Scholar
  52. 52.
    Hanna, M.M., Methods Enzymol., 1989, vol. 180, pp. 383–409.PubMedGoogle Scholar
  53. 53.
    Hori, N., Iwai, S., Inoue, H., and Ohtsuka, E., Biol. Chem., 1992, vol. 267, pp. 15591–15594.Google Scholar
  54. 54.
    Doring, T., Mitchell, P., Osswald, M., Bochkariov, D., and Brimacombe, R., EMBO J., 1994, vol. 13, pp. 2677–2685.PubMedGoogle Scholar
  55. 55.
    Bochkarev, D.E., Study on the Interaction of tRNA with Ribosome by Pulse Photoaffinity Crosslinking, Cand. Sci. (Chem.) Dissertation, Pushchino: Moscow State Univ., 1993.Google Scholar
  56. 56.
    Sergiev, P., Dokudovskaya, S., Romanova, E., Topin, A., Bogdanov, A., Brimakombe, R., and Dontsova, O., Nucleic Acids Res., 1998, vol. 26, pp. 2519–2525.PubMedGoogle Scholar
  57. 57.
    Sylvers, L.A. and Wower, J., Bioconj. Chem., 1993, vol. 4, pp. 411–418.Google Scholar
  58. 58.
    Braun, B.R., Bartholomew, B., Kassavetis, G.A., and Geiduschek, E.P., J. Mol. Biol., 1992, vol. 228, pp. 1063–1077.PubMedGoogle Scholar
  59. 59.
    Sergiev, P.V., Lavrik, I.N., Dokudovskaya, S.S., Dontsova, O.A., and Bogdanov, A.A., Biokhimiya, 1998, vol. 63, pp. 1129–1143.Google Scholar
  60. 60.
    Bhangu, R. and Wollenzien, P., Biochemistry, 1992, vol. 31, pp. 5937–5944.PubMedGoogle Scholar
  61. 61.
    Dontsova, O., Dokudovskaya, S., Kopylov, A., Bogdanov, A., Rinke-Appel, J., Junke, N., and Brimacombe, R., EMBO J., 1992, vol. 11, pp. 3105–3116.PubMedGoogle Scholar
  62. 62.
    Brimacombe, R., Mitchell, P., Osswald, M., and Bochkariov, D., FASEB J., 1993, vol. 7, pp. 161–167.PubMedGoogle Scholar
  63. 63.
    Chen, J.K., Frank, L.A., Hixson, S.S., and Zimmermann, R.A., Biochemistry, 1985, vol. 24, pp. 4777–4784.PubMedGoogle Scholar
  64. 64.
    Brimacombe, R., Biochimie, 1991, vol. 73, pp. 927–936.PubMedGoogle Scholar
  65. 65.
    Sergiev, P.V., Lavrik, I.N., Wlasoff, V.A., Dokudovskaya, S.S., Dontsova, O.A., Bogdanov, A.A., and Brimakombe, R., RNA, 1997, vol. 3, pp. 464–475.PubMedGoogle Scholar
  66. 66.
    Baranov, P.V., Kubarenko, A.V., Gurvich, O.L., Shamolina, T.A., and Brimacombe, R., Nucleic Acids Res., 1999, vol. 27, pp. 184–185.PubMedGoogle Scholar
  67. 67.
    Nassal, M., J. Am. Chem. Soc., 1984, vol. 106, pp. 7540–7545.Google Scholar
  68. 68.
    Shih, L. and Bayley, H., Anal. Biochem., 1985, vol. 144, pp. 132–141.PubMedGoogle Scholar
  69. 69.
    Baldini, G., Martoglio, B., Schachenmann, A., Zugliani, C., and Brunner, J., Biochemistry, 1988, vol. 27, pp. 7951–7959.PubMedGoogle Scholar
  70. 70.
    Baldwin, J.E., Pratt, A.J., and Moloney, M.G., Tetrahedron, 1987, vol. 43, pp. 2565–2575.Google Scholar
  71. 71.
    Falchetto, R., Vorherr, T., Brunner, J., and Carafoli, E., J. Biol. Chem., 1991, vol. 266, pp. 2930–2936.PubMedGoogle Scholar
  72. 72.
    Beck-Sickiger, A.G., Wieland, H.A., and Brunner, J., Recept. Res., 1995, vol. 15, pp. 473–485.Google Scholar
  73. 73.
    Ploug, M., Ostergaard, S., Hansen, L. B., Holm, A., and Dano, K., Biochemistry, 1998, vol. 37, pp. 3612–3622.PubMedGoogle Scholar
  74. 74.
    Topin, A.N. and Korshunova, G.A., Vestn. Mosk. Univ., Ser. 2: Khim., 1995, vol. 36, pp. 583–587.Google Scholar
  75. 75.
    Topin, A.N. and Korshunova, G.A., Programme and Abstracts, 23rd European Peptide Symposium, Braga (Portugal), 1994, no. 3–87, p. 121.Google Scholar
  76. 76.
    Bondar', D.A., Synthesis and Properties of New Photoactivatable Multifunctional Reagents Containing Aryl(trifluoromethyl)diazirine Group, Graduate Research Work, Moscow: Chemistry Dept., Moscow State Univ., 1999.Google Scholar
  77. 77.
    Kubarenko, A.V., Study of the Functional Topography of Elongation Factor G on E. coli Ribosome with the Use of Chemical Photoaffinity Modification, Graduate Research Work, Moscow: Chemistry Dept., Moscow State Univ., 2000.Google Scholar
  78. 78.
    Anthony-Cahill, S., Griffith, M., Noren, C., Suich, D., and Schultz, P., TIBS, 1989, vol. 14, pp. 400–403.PubMedGoogle Scholar
  79. 79.
    Kurzchalia, T.V., Wiedmann, M., Girshovich, A.S., Bochkareva, E.S., Bielka, H., and Rapoport, T.A., Nature, 1986, vol. 320, pp. 634–636.PubMedGoogle Scholar
  80. 80.
    Krieg, U.C., Walter, P., and Johnson, A.E., Proc. Natl. Acad. Sci. USA, 1986, vol. 83, pp. 8604–8608.PubMedGoogle Scholar
  81. 81.
    Kemp, D.S. and Galakatos, N.G., J. Org. Chem., 1986, vol. 51, pp. 1821–1829.Google Scholar
  82. 82.
    Kogon, A.A., Novel Photoactivatable Reagents for Studying Biological Macromolecules by Fast Photoaffinity Crosslinking, Cand. Sci. (Chem.) Dissertation, Moscow: Moscow State Univ., 1992.Google Scholar
  83. 83.
    Savage, M.D., Mattson, G., Desai, S., Nielander, G.W., Morgensen, S., and Conklin, E.J., Avidin-Biotin Chemistry: A Handbook, Illinois: Pierce Chemical Co., 1992.Google Scholar
  84. 84.
    Kogon, A., Peletskaya, E., Quinn, T., and Folk, W., Book of Abstracts, 37th Annual West Central States Biochemistry and Molecular Biology Conference, Research and Education, University of Missouri-Columbia, 1994, p. 60.Google Scholar
  85. 85.
    Brunner, J., Trends in Cell Biol., 1996, vol. 6, pp. 154–157.Google Scholar
  86. 86.
    Blanton, M.P., McCardy, E.A., Huggins, A., and Parikh, D., Biochemistry, 1998, vol. 37, pp. 14545–14555.PubMedGoogle Scholar
  87. 87.
    Bochkarev, D. and Kogon, A., Anal. Biochem., 1992, vol. 204, pp. 90–95.PubMedGoogle Scholar
  88. 88.
    Kogon, A., Bochkarev, D., Baskunov, B., and Cherpakov, A., Liebigs Ann. Chem., 1992, pp. 879–881.Google Scholar
  89. 89.
    Kempin, U., Kanoaka, Y., and Hatanaka, Y., Heterocycles, 1998, vol. 49, pp. 465–468.Google Scholar
  90. 90.
    Rimoldi, J.M., Kingston, D.G.I., Chaudhary, A.G., Samaranayake, G., Grover, S., and Hamel, E., J. Nat. Prod., 1993, vol. 56, pp. 1313–1330.PubMedGoogle Scholar
  91. 91.
    Hatanaka, Y., Yoshiba, E., Hakayama, H., and Kanaoka, Y., Bioorg. Chem., 1989, vol. 17, pp. 482–485.Google Scholar
  92. 92.
    Pillai, K., Synthesis, 1980, pp. 1–26.Google Scholar
  93. 93.
    Lloyd-Williamsetal, F., Tetrahedron, 1993, vol. 49, pp. 11065–11133.Google Scholar
  94. 94.
    Olejnik, J., Krzymanska-Olejnik, E., and Rothschild, K.J., Nucleic Acids Res., 1998, vol. 26, pp. 3572–3576.PubMedGoogle Scholar
  95. 95.
    Wei, Y., Yan, Y., Pei, D., and Gong, B., Bioorg. Med. Chem. Letters, 1998, vol. 8, pp. 2419–2422.Google Scholar
  96. 96.
    Olejnik, J., Ludemann, H.-C., Krzymanska-Olejnik, E., Berkenkamp, S., Hillenkamp, F., and Rothschild, K.J., Nucleic Acids Res., 1999, vol. 27, pp. 4626–4631.PubMedGoogle Scholar
  97. 97.
    Patchornik, A., Amit, S., and Woodward, R.B., J. Am. Chem. Soc., 1970, vol. 92, pp. 6333–6335.Google Scholar
  98. 98.
    Fang, K., Hashimoto, M., Jockusch, S., Turro, N.J., and Nakanishi, K., J. Am. Chem. Soc., 1998, vol. 120, pp. 8543–8544.Google Scholar
  99. 99.
    Hatanaka, Y., Hashimoto, M., Kurihara, H., Nakayama, H., and Kanaoka, Y., J. Org. Chem., 1994, vol. 59, pp. 383–387.Google Scholar
  100. 100.
    Utkin, Y.N., Hatanaka, Y., Franke, P., Machold, J., Hucho, F., and Tsetlin, V.I., J. Protein Chem., 1995, vol. 14, pp. 197–203.PubMedGoogle Scholar

Copyright information

© MAIK “Nauka/Interperiodica” 2000

Authors and Affiliations

  • G. A. Korshunova
    • 1
    • 2
  • N. V. Sumbatyan
    • 1
    • 2
  • A. N. Topin
    • 1
    • 2
  • M. T. Mtchedlidze
    • 1
    • 2
  1. 1.Belozersky Institute of Physico-Chemical BiologyMoscow State UniversityMoscowRussia
  2. 2.Chemical FacultyMoscow State UniversityMoscowRussia

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